R/deprecated.R

In russHyde/miiq: Microarrays Are Awesome: Get Them Analysed HERE!

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#' limma workflow: .....
#'
#' @param        gset          An ExpressionSet
#' @param        design_fn   A function that creates a design matrix based on
#'   gset as input.
#' @param        contrast_fn   A function that creates a contrasts matrix
#'   based on an input design matrix.
#'
#' @return       A list(design, contrast, fits_init, fits).
#'
#' @include      diffex_classes.R   diffex_methods.R
#' @export

limma_workflow <- function(
                           gset = NULL,
                           design_fn = NULL,
                           contrast_fn = NULL) {
  message("Deprecated: limma_workflow; use run_diffex_workflow()")
  run_diffex_workflow(
    gset, DiffexConfig(design_fn, contrast_fn)
  )
}

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#' Builds a function that returns the col indices of the desired samples
#'
#' Creates a function that can be applied to a geo-limma-dataset
#'   or to an ExpressionSet, and returns the column indices of those
#'   samples that are to kept
#' This just reduces the boilerplate involved in checking g-l-d or
#'   ExpressionSet nature of the input
#'
#' @param        column.filter.fn   Function that decides which samples to keep
#'
#' @include      utils.R
#' @export
#'

gld_fnBuilder_keepSample <- function(
                                     column.filter.fn
) {
  stopifnot(is.function(column.filter.fn))
  fn <- column.filter.fn

  function(
             geo.limma.dataset = NULL,
             gset = NULL) {
    warning("deprecation warning: recommend using a function(gset)")
    gset <- .check_or_get_eset(geo.limma.dataset, gset)
    keep_cols <- fn(gset)
    keep_cols
  }
}

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#' Function for filtering on microarray probes
#'
#' @param        geo.limma.dataset   An eset.limma.dataset
#' @param        gset          An ExpressionSet (overrides use of
#'   geo.limma.dataset)
#'
#' @include      utils.R   filter_functions.R
#' @export
#'
keep_probe_fn <- function(
                          geo.limma.dataset = NULL,
                          gset = NULL) {
  warning(
    "`miiq::keep_probe_fn` is deprecated, please use",
    "`miiq::keep_all_entrez_probes`"
  )

  gset <- .check_or_get_eset(geo.limma.dataset, gset)

  keep_all_entrez_probes(gset)
}

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#' Default function for choosing which samples to keep in a ESet / g-l-d
#'
#' @param        geo.limma.dataset   An eset_limma_dataset.
#' @param        gset          An ExpressionSet - used preferentially
#'   over ELD@eset.
#'
#' @importFrom   Biobase       sampleNames
#' @include      filter_functions.R
#' @export
#'

gld_fnDefault_keepSample <- gld_fnBuilder_keepSample(
  column.filter.fn = keep_all_samples
)

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#' Default function for choosing which probes to keep in an ESet / g-l-d
#'
#' @param        geo.limma.dataset   A geo_limma_dataset
#' @param        gset          An ExpressionSet
#'
#' @importFrom   Biobase       featureNames
#'
#' @include      utils.R   filter_functions.R
#' @export
#'

gld_fnDefault_keepProbe <- function(
                                    geo.limma.dataset = NULL,
                                    gset = NULL) {
  warning(
    "`miiq::gld_fnDefault_keepProbe` is deprecated, please use",
    "`miiq::keep_all_probes`"
  )
  # TODO: replace argnames with the lint-passing `geo_limma_dataset`
  gset <- .check_or_get_eset(geo.limma.dataset, gset)

  keep_all_probes(gset)
}

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#' Builds a function that makes the design matrix for a dataset
#'
#' User passes in the column labels of the phenoData that are to be used in
#'   making the design
#' And passes in a design.function that converts these columns into the design
#' The functionBuilder checks for the validity of the input (treatment.cols /
#'   design.function) and the built function checks the validity of the
#'   ExpressionSet / geo-limma-dataset that was passed in
#'
#' @param        treatment.cols   Which columns of the pData should be kept?
#' @param        design.fn     Function for making design matrices.
#'
#' @importFrom   Biobase       pData   sampleNames
#'
#' @include      utils.R   diffex_functions.R
#' @export
#'

gld_fnBuilder_exptDesign <- function(
                                     treatment.cols = NULL,
                                     design.fn = NULL) {
  design_function <- function(
                                geo.limma.dataset = NULL,
                                gset = NULL) {
    warning(
      "Creating design-makers using `miiq::gld_fnBuilder_exptDesign` is",
      "deprecated. Please use `miiq::design_builder` instead."
    )
    design_builder(
      treatment_cols = treatment.cols, design_fn = design.fn
    )(
      gset = .check_or_get_eset(geo.limma.dataset, gset)
    )
  }

  design_function
}

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#' Default function for setting up an expt design from the pData of the
#'   ExpressionSet
#'
#' Just takes the "title" column of the pData and uses it as a factor.
#'
#' @param        geo.limma.dataset   A geo_limma_dataset.
#' @param        gset          An ExpressionSet.
#'
#' @export
#'

gld_fnDefault_exptDesign <- gld_fnBuilder_exptDesign(
  treatment.cols = "title",
  design.fn = function(treatments) {
    title <- treatments[, 1]
    model.matrix(~title)
  }
)

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